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.tar files Microarray

Good afternoon,

Can you please advise me on the following:

I have downloaded a GSE13067_RAW.tar from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi. This file contains CEL.gz files (e.g. GSM327282.CEL.gz). I tried this instructions to load them into RStudio https://www.rpubs.com/billchenxi/BioInfo_R_Ch5 however I am getting the following error:

No cel filennames specified and no cel files in specified directory

When trying

myData <- ReadAffy(celfile.path="..../GSE13067_RAW.tar/")

Any idea? Maybe I first need to "untar" the GSE13067_RAW.tar somehow?

Thanks a lot!

microarray
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written by Nona • Nona

1 answer

tar is a storage format. You have to unpack it first. tar xf GSE13067_RAW.tar and then read the CEL files within (if present). Or use a GUI such as 7z for untaring if you're unfamiliar with command line. macOS does that out of the box by double-clicking the tarball.

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written by ATpoint ATpoint

Thank you very much for your response. And there is no way to do this directly in R Studio?

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written by Nona • Nona

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